[BioC] Repeated Measures mRNA expression analysis

[Mike Love]

Hi Charles,

On Jun 24, 2013, at 10:08 PM, Charles Determan Jr <deter088 at umn.edu> wrote:

> 
> design(dds) <- formula(~ time + treatment)
> 
> Is this what is considered the appropriate way to address repeated measures
> in mRNA expression experiments?  Any thoughts are appreciated.
> 

Yes, this is the correct design formula for DESeq2 for estimating and testing the effect of treatment over all time points. We use by default a Wald test, and the likelihood ratio test is also implemented (see vignette). This is then a similar approach to calling anova.glm() on a glm fit for a single gene.

Best,

Mike